Will each set of barbarians be treated as a seperate new civ. Or will they just be a more generic menace.

As well will it be possible to have new civs appear with a slightly below average set of techs. This would allow for the fact that propogated scientific knowledge will become the basic starting level.

A comment on Barbarians

The way I see it what we label as barbarians are just tribal cultures neighbouring more complex social societies with higher tech.
The social model and tech model should somehow simulate these realities. Hard techs should easely be transfered while social advances should have a certain social structure as a prerequisite (everybody knows that techs are faster to achieve and develop than social, cultural changes).

Take Rome and the germanic peoples. Rome had a quite advanced society, it went from the military to the entertainment advances.
The german on the other hand had a strong tribal organization, their social structure did evolve as they became more sedentarized (mainly agricultural advances aquired through trade contact from rome) but they were way behind the romans on that aspect. On the other hand when you compare their military organization and power in cent. 1-2 AD with 5th century they cought up really fast (ex. The Gots organized heavy infantry tactics), never becoming top roman legions equal but still much better than before.
Now just add another "small" factor, numbers. A tribal society is much easier to mobilize massively than a urbanized one.
The germans aquired enough tech so that, with their numbers, once the romans showed a hole they would storm through (and so it happened).

Bottom line. if social-tech-military model conections are well established you will have barbarians and advanced civs banging heads all the time.

Barbarians... will have cultures all their own, we will need special rules to make pastoral barbarians work right

New civs... cultures will have their own tech levels, when a culture gets promoted to a civ, it will inherit the previous tech level. Frequently the tech level of cultures will be significantly below that of nearby civs, but not always. (I see Henrique already figured this out!) We are trying to get diffusion of technology to work reasonably well.

Merging civs... absolutely!

Logo:

I don't know why anyone would prefer to play as a single city state. You are almost certain to get swallowed up eventually. However the government model can handle the player running a Group of semi-autonomous City states.

Henrique:

On civs never lasting forever... We had a big discussion on this a ways back. I tried to search for it but couldn't find it. Our basic framework at the moment is:
1. When a revolution starts the player can pick either side for them to run (some care is needed here)
2. If your civilization is conquered from the outside, if your people try to "throw the bums out" you run the "resistance" and regain your civilization if the rebellion is successful.
3. If your civilization conquers an area that is too large to hold in a unified fashion given that technology or other factors, you can arbitrarily split it and rule whichever party you want.
4. There may be other rules needed...

These rules allow for the player to stay in the game over transitions like Norsemen become (3) Normans who become (3) English who become (1) Americans.

If I understand well you have all the corners taken care of except one.

1 - one VERY frequent thing to happen should be a civ being runned over, killed, dead, kaput (well - things close to GENOCIDE/forced migration/slavery etc).
Big invasions where reasonably frequent and more stable frontiers only started to get a definitive form when Nationalism became a cultural characteristic. So civs prior to nationalism (and all the tech social diplomatic advances that come before and after) should accept that the end might be just arround the corner.

My idea on this is that when there is no way you can get back on top of your civ, you should be given the chance of playing a AI controlled culture/civ that resembles the most the one you lost (geographic and ethnic affinity should be the big factors). This way you would get the - I was the saxons now I am the normans felling.

I would say that you should change Civs at most about twice in the gameeven if this is not realistic it seems morelike it should work for me. Or possibly could this be optional like set it to high number of chages, etc

Find me a civilization that endured from pre-history to modern days and I will agree with you. My guess is there arent any. With the rebellion option (the you get conquered then you revolt thing) the only civs I remember that would be simulated by the game are China and Japan (maybe there are more, I am not sure)
Remember all the ocidental countries were built on the ashes of other cultures.
Now I wouldnt like to keep losing just for the sake of realism but if there is a way to keep the flow/fun of the game and allow for the rise and fall of empires then Iīll be happy.